******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.0.0 (Release date: 2008-07-12 05:23:09 +1000 (Sat, 12 Jul 2008)) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/INO_up800.s ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ CHO1 1.0000 800 CHO2 1.0000 800 FAS1 1.0000 800 FAS2 1.0000 800 ACC1 1.0000 800 INO1 1.0000 800 OPI3 1.0000 800 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/INO_up800.s -text -mod zoops -dna -revcomp -bfile /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/yeast.nc.6.freq -x_branch -nostatus -nmotifs 2 -minw 8 model: mod= zoops nmotifs= 2 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 7 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= yes wbranch= no bfactor= 3 heapsize= 64 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 5600 N= 7 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/yeast.nc.6.freq): A 0.324 C 0.176 G 0.176 T 0.324 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 17 sites = 7 llr = 117 E-value = 2.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :1:1::a::1:9a77:: pos.-specific C 1:4:3a:::::::::3: probability G 69467:::a:a1:3141 matrix T 3:13:::a:9::::139 bits 2.5 * * * 2.3 * * * 2.0 * * * 1.8 * ** * * Relative 1.5 * ***** * * Entropy 1.3 * ***** *** * (24.1 bits) 1.0 ** ********** * 0.8 ************** ** 0.5 ***************** 0.3 ***************** 0.0 ----------------- Multilevel GGCGGCATGTGAAAAGT consensus T GTC G C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------------- INO1 + 619 4.64e-10 GGCGGCTAAA TGCGGCATGTGAAAAGT ATTGTCTATT FAS1 - 91 6.11e-09 TGCTTGGCTG GGCGGCATGTGAAGTTT TTGGCCGTCG CHO2 - 350 6.52e-09 GAATAATGAA TGCGGCATGAGAAAAGT GTGGCAATTG ACC1 - 79 1.20e-08 CGCGCGCGGC CGGGCCATGTGAAGATT TTAACGGGCG CHO1 - 636 1.20e-08 ATCTTTAGAT GGGTCCATGTGAAAGCT CAAAGGCGTG OPI3 + 584 3.84e-08 GTGTCAATGA GAGTGCATGTGGAAAGT TGCACCGGTT FAS2 - 563 5.67e-08 AGGCGAATGA GGTAGCATGTGAAAACG CGGGAGATAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- INO1 4.6e-10 618_[+1]_165 FAS1 6.1e-09 90_[-1]_693 CHO2 6.5e-09 349_[-1]_434 ACC1 1.2e-08 78_[-1]_705 CHO1 1.2e-08 635_[-1]_148 OPI3 3.8e-08 583_[+1]_200 FAS2 5.7e-08 562_[-1]_221 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=17 seqs=7 INO1 ( 619) TGCGGCATGTGAAAAGT 1 FAS1 ( 91) GGCGGCATGTGAAGTTT 1 CHO2 ( 350) TGCGGCATGAGAAAAGT 1 ACC1 ( 79) CGGGCCATGTGAAGATT 1 CHO1 ( 636) GGGTCCATGTGAAAGCT 1 OPI3 ( 584) GAGTGCATGTGGAAAGT 1 FAS2 ( 563) GGTAGCATGTGAAAACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 17 n= 5488 bayes= 9.61287 E= 2.6e-002 -945 -30 170 -18 -118 -945 229 -945 -945 129 129 -118 -118 -945 170 -18 -945 70 202 -945 -945 251 -945 -945 162 -945 -945 -945 -945 -945 -945 162 -945 -945 251 -945 -118 -945 -945 140 -945 -945 251 -945 140 -945 -30 -945 162 -945 -945 -945 114 -945 70 -945 114 -945 -30 -118 -945 70 129 -18 -945 -945 -30 140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 17 nsites= 7 E= 2.6e-002 0.000000 0.142857 0.571429 0.285714 0.142857 0.000000 0.857143 0.000000 0.000000 0.428571 0.428571 0.142857 0.142857 0.000000 0.571429 0.285714 0.000000 0.285714 0.714286 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.000000 1.000000 0.000000 0.857143 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.000000 0.285714 0.000000 0.714286 0.000000 0.142857 0.142857 0.000000 0.285714 0.428571 0.285714 0.000000 0.000000 0.142857 0.857143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT]G[CG][GT][GC]CATGTGAA[AG]A[GCT]T -------------------------------------------------------------------------------- Time 31.59 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 10 sites = 7 llr = 81 E-value = 4.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::31::a:6: pos.-specific C :a:::a:911 probability G 1::9a:::19 matrix T 9:7::::11: bits 2.5 * ** 2.3 * ** 2.0 * ** * 1.8 * *** * * Relative 1.5 * ***** * Entropy 1.3 ** ***** * (16.8 bits) 1.0 ** ***** * 0.8 ******** * 0.5 ******** * 0.3 ********** 0.0 ---------- Multilevel TCTGGCACAG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- OPI3 - 186 3.28e-07 GAAAACCAGA TCTGGCACAG ACCGTTGTCA ACC1 + 232 3.28e-07 CCAGTCGTAT TCTGGCACAG TATAGCCTAG CHO1 - 559 3.28e-07 ATATTCAGTG TCTGGCACAG AAGTCTGCAC FAS1 + 44 5.16e-06 TACACGAGGT GCAGGCACGG TTCACTACTC FAS2 - 185 6.97e-06 TTCTTGCTTT TCTGGCACTC TTGACGGCTT CHO2 - 413 6.97e-06 TTTTGCCGTT TCTGGCATCG CCGTTCATTT INO1 + 332 8.18e-06 CAGAGGAATC TCAAGCACAG CCTCCAGCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- OPI3 3.3e-07 185_[-2]_605 ACC1 3.3e-07 231_[+2]_559 CHO1 3.3e-07 558_[-2]_232 FAS1 5.2e-06 43_[+2]_747 FAS2 7e-06 184_[-2]_606 CHO2 7e-06 412_[-2]_378 INO1 8.2e-06 331_[+2]_459 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=10 seqs=7 OPI3 ( 186) TCTGGCACAG 1 ACC1 ( 232) TCTGGCACAG 1 CHO1 ( 559) TCTGGCACAG 1 FAS1 ( 44) GCAGGCACGG 1 FAS2 ( 185) TCTGGCACTC 1 CHO2 ( 413) TCTGGCATCG 1 INO1 ( 332) TCAAGCACAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 5537 bayes= 10.2321 E= 4.4e+001 -945 -945 -30 140 -945 251 -945 -945 -18 -945 -945 114 -118 -945 229 -945 -945 -945 251 -945 -945 251 -945 -945 162 -945 -945 -945 -945 229 -945 -118 82 -30 -30 -118 -945 -30 229 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 7 E= 4.4e+001 0.000000 0.000000 0.142857 0.857143 0.000000 1.000000 0.000000 0.000000 0.285714 0.000000 0.000000 0.714286 0.142857 0.000000 0.857143 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.571429 0.142857 0.142857 0.142857 0.000000 0.142857 0.857143 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TC[TA]GGCACAG -------------------------------------------------------------------------------- Time 62.82 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CHO1 1.89e-07 558_[-2(3.28e-07)]_38_[-1(2.43e-05)]_12_[-1(1.20e-08)]_148 CHO2 1.91e-06 349_[-1(6.52e-09)]_46_[-2(6.97e-06)]_378 FAS1 1.35e-06 43_[+2(5.16e-06)]_37_[-1(6.11e-09)]_693 FAS2 1.45e-05 184_[-2(6.97e-06)]_368_[-1(5.67e-08)]_221 ACC1 1.89e-07 78_[-1(1.20e-08)]_136_[+2(3.28e-07)]_559 INO1 1.82e-07 331_[+2(8.18e-06)]_207_[+1(9.62e-05)]_4_[+1(5.31e-05)]_32_[+1(4.64e-10)]_165 OPI3 5.70e-07 185_[-2(3.28e-07)]_388_[+1(3.84e-08)]_32_[-1(3.61e-05)]_151 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 2 reached. ******************************************************************************** CPU: tlb-sayonara.imb.uq.edu.au ********************************************************************************